17-40331276-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_000964.4(RARA):c.58C>G(p.Pro20Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000278 in 1,613,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00030 ( 0 hom. )
Consequence
RARA
NM_000964.4 missense
NM_000964.4 missense
Scores
8
6
Clinical Significance
Conservation
PhyloP100: 6.92
Genes affected
RARA (HGNC:9864): (retinoic acid receptor alpha) This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, RARA
BP4
?
Computational evidence support a benign effect (MetaRNN=0.29652977).
BS2
?
High AC in GnomAd at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RARA | NM_000964.4 | c.58C>G | p.Pro20Ala | missense_variant | 2/9 | ENST00000254066.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RARA | ENST00000254066.10 | c.58C>G | p.Pro20Ala | missense_variant | 2/9 | 1 | NM_000964.4 | P4 | |
RARA | ENST00000425707.7 | c.58C>G | p.Pro20Ala | missense_variant | 2/7 | 1 | |||
RARA | ENST00000394089.6 | c.58C>G | p.Pro20Ala | missense_variant | 2/9 | 2 | P4 | ||
RARA | ENST00000577646.5 | c.58C>G | p.Pro20Ala | missense_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152202Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000878 AC: 22AN: 250696Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135590
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GnomAD4 exome AF: 0.000298 AC: 435AN: 1461636Hom.: 0 Cov.: 31 AF XY: 0.000294 AC XY: 214AN XY: 727136
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GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74350
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.58C>G (p.P20A) alteration is located in exon 2 (coding exon 1) of the RARA gene. This alteration results from a C to G substitution at nucleotide position 58, causing the proline (P) at amino acid position 20 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T;T;T
Polyphen
0.32
.;B;B;.
Vest4
0.49, 0.56
MVP
MPC
0.92
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at